Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
  • C07K16/2818—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against CD28 or CD152
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P37/00—Drugs for immunological or allergic disorders
  • A61P37/02—Immunomodulators
  • A61P37/04—Immunostimulants
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
  • A61K39/39533—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals
  • A61K39/3955—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals against proteinaceous materials, e.g. enzymes, hormones, lymphokines
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
  • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/55—Fab or Fab'
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
  • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

• the invention provides monoclonal antibodies that specifically bind to PD-1 and therapeutic compositions thereof.
• the agents enhance T cell and NK cell function to increase cell and cytokine mediated immunity for the treatment of various immune dysfunction related disorders including cancers and infectious diseases.
• PD-1 is a member of the CD28 family of receptors comprising CD28, CTLA-4, PD-1, ICOS, and BTLA (Freeman et al. (2000) J Exp Med 192: 1027-34; Latchman et al. (2001) Nat Immunol 2:261-8).
• PD-1 is an inducible immunosuppressive receptor mainly upregulated on activated T cells and B cells during the progression of immunopathological conditions.
• PD-1 interaction with its ligand PD-Ll results in the inhibition of TCR and BCR mediated proliferation and cytokine production and induction of apoptosis of antigen specific T cells through the intrinsic PD-1 mediated negative signaling of an immunoreceptor tyrosine-based inhibitory motif (ITIM) (Agata et al. (1996) Int. Immunol. 8:765, Unkeless and Jin. (1997) Curr. Opin. Immunol. 9:338-343, Okzaki et al. (2001) PNAS 98: 13866-71, Dong et al. (2002) Nat. Med. 8:793-800).
• ITIM immunoreceptor tyrosine-based inhibitory motif
• PD-Ll is also inducible on lymphoid tissues and non-lymphoid peripheral tissues following cellular activation.
• PD-Ll is upregulated in a variety of affected cell types including cancer and stromal cells in addition to immune cells, and plays an active role in immunosuppression during the course of the deterioration of diseases (Iwai et al (2002) PNAS 99: 12293-7, Ohigashi et al. (2005) Clin Cancer Res 11 :2947-53).
• PD-Ll upregulation has been linked to poor clinical outcomes in a variety of cancers and viral infection (Hofmeyer et al. (2011) J. BioMed. Biotech. 2011 : 1-9, McDermott and Atkins. (2013) Cancer Med. 2:662-73).
• the PD-1 antibodies of the present invention are used as an antibody
• immunomodulating agent and may be efficacious when used as monotherapy or when combined with antibodies to other immunosuppressive molecules.
• the present invention provides antibodies and binding proteins that bind to PD-1.
• the antibodies bind to PD-1 and block interaction with PD-Ll . By blocking the interaction of PD-1 with PD-Ll, such antibodies are useful to reduce or inhibit immunosuppression.
• the invention provides an antibody or fragment that binds to PD-1, which comprises a heavy chain variable domain which comprises SEQ ID NO: 6, SEQ ID NO: 16, SEQ ID NO: 26, or SEQ ID NO: 36.
• the heavy chain variable domain is at least 80%, or at least 85%, or at least 90%, or at least 95% identical to SEQ ID NO: 6, SEQ ID NO: 16, SEQ ID NO: 26, SEQ ID NO: 36.
• the antibodies may further comprise a light chain variable domain which comprises SEQ ID NO: 10, SEQ ID NO: 20, SEQ ID NO: 30, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 68, SEQ ID NO: 72, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 88, SEQ ID NO: 92, SEQ ID NO: 96, SEQ ID NO: 100, SEQ ID NO: 104, SEQ ID NO: 108, SEQ ID NO: 112, SEQ ID NO: 116, SEQ ID NO: 120, SEQ ID NO: 124, SEQ ID NO: 128, SEQ ID NO: 132, SEQ ID NO: 136, SEQ ID NO: 140, SEQ ID NO: 144, SEQ ID NO: 148, SEQ ID NO: 152, SEQ ID NO:
• the light chain variable domain is at least 80%, or at least 85%, or at least 90%, or at least 95% identical to SEQ ID NO: 10, SEQ ID NO: 20, SEQ ID NO: 30, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 68, SEQ ID NO: 72, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 88, SEQ ID NO: 92, SEQ ID NO: 96, SEQ ID NO: 100, SEQ ID NO: 104, SEQ ID NO: 108, SEQ ID NO: 112, SEQ ID NO: 116, SEQ ID NO: 120, SEQ ID NO: 124, SEQ ID NO: 128, SEQ ID NO: 132, SEQ ID NO: 136, SEQ ID NO: 140, SEQ ID NO: 144, SEQ ID NO:
• the invention provides an antibody or fragment thereof that binds to PD-1, wherein the heavy chain comprises a CDR-IH (Kabat) which has SEQ ID NO: 1, SEQ ID NO: 11, SEQ ID NO: 21, or SEQ ID NO: 31, a CDR-2H (Kabat) which has SEQ ID NO: 3, SEQ ID NO: 13, SEQ ID NO: 23, or SEQ ID NO: 33, and a CDR- 3H which has SEQ ID NO: 5, SEQ ID NO: 15, SEQ ID NO: 25, or SEQ ID NO: 35.
• the invention provides an antibody or fragment thereof that binds to PD-1, wherein the heavy chain comprises a CDR-IH (Chothia) which has SEQ ID NO: 2, SEQ ID NO: 12, SEQ ID NO: 22, or SEQ ID NO: 32, a CDR-2H (Chothia) which has SEQ ID NO: 4, SEQ ID NO: 14, SEQ ID NO: 24, or SEQ ID NO: 34, and a CDR-3H which has SEQ ID NO: 5, SEQ ID NO: 15, SEQ ID NO: 25, or SEQ ID NO: 35.
• CDR-IH Chothia
• SEQ ID NO: 12 which has SEQ ID NO: 12
• SEQ ID NO: 22 which has SEQ ID NO: 4
• SEQ ID NO: 14 SEQ ID NO: 14
• SEQ ID NO: 34 SEQ ID NO: 34
• CDR-3H which has SEQ ID NO: 5
• SEQ ID NO: 15 SEQ ID NO: 25
• SEQ ID NO: 35 SEQ ID NO: 35
• the invention provides an antibody or fragment thereof that binds to PD-1, wherein the light chain comprises a CDR-1L which has SEQ ID NO: 7, SEQ ID NO: 17, SEQ ID NO: 27, SEQ ID NO: 37, SEQ ID NO: 41, SEQ ID NO: 45, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 57, SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 69, SEQ ID NO: 73, SEQ ID NO: 77, SEQ ID NO: 81, SEQ ID NO: 85, SEQ ID NO: 89, SEQ ID NO: 93, SEQ ID NO: 97, SEQ ID NO: 101, SEQ ID NO: 105, SEQ ID NO: 109SEQ ID NO: 113, SEQ ID NO: 117, SEQ ID NO: 121, SEQ ID NO: 125, SEQ ID NO: 129, SEQ ID NO: 133, SEQ ID NO: 137, SEQ ID NO:
• the invention also provides conjugates of the antibodies, for example, and without limitation, to imaging agents, therapeutic agents, or cytotoxic agents.
• compositions comprising the antibodies and conjugates and a pharamaceutically acceptable carrier.
• the invention provides a method of inhibiting the interaction of PD-1 with PD-L1 in a subject, which comprises administering an effective amount of an antibody or fragment of the invention.
• the invention further provides a method of inhibiting
• the invention further provides a method of stimulating an immune response against a cell or tissue that expresses PD-1, which comprises administering to a subject an effective amount of the antibody or fragment of the invention.
• the cell or tissue that expresses PD-1 is a neoplastic cell or an infected cell.
• Figure 1 depicts binding to anti-hFc of antibodies R3 Al, R3 A2, R4B3, R3B7, and R3D6.
• Figure 2 depicts binding to EGFR-Fc of antibodies R3 Al, R3 A2, R4B3, R3B7, and R3D6.
• Figure 3 depicts binding to ckit-Fc of antibodies R3 Al, R3 A2, R4B3, R3B7, and R3D6.
• Figure 4 depicts binding to KDR-Fc of antibodies R3 Al, R3 A2, R4B3, R3B7, and R3D6.
• Figure 5 depicts binding to hPD-l-Fc of antibodies R3A1, R3A2, R4B3, R3B7, and R3D6.
• Figure 6 depicts blocking of PD-L1 to hPD-1 by antibodies R3A1, R3A2, R4B3, R3B7, and R3D6.
• Figure 7 depicts binding to mPD-l-Fc of antibodies R3 Al, R3 A2, R4B3, R3B7, and R3D6.
• Figure 8 depicts binding to PD-l-Fc of antibodies A2_#l and A2_#2.
• Figure 9 depicts blocking of PD-L1 to hPD-1 by antibodies A2_#l and A2_#2.
• Figure 10 depicts blocking of PD-L2 to hPD-1 by antibodies A2_#l and A2_#2.
• Figure 11 depicts binding of activity to hPD-1 expressing HEK293 cells as measured by flow cytometry of antibodies A2_#l and A2_#2.
• Figure 12 depicts binding activity to hPD-1 expressing CD4 T cells as measured by flow cytometry of antibodies A2_#l and A2_#2.
• Figure 13 depicts binding activity to hPD-1 expressing CD8 T cells as measured by flow cytometry of antibodies A2_#l and A2_#2.
• Figure 14 depicts JL2 secretion in SEB stimulated PBMC cultured with antibodies A2_#l and A2_#2.
• Figure 15 depicts INFy secretion in SEB stimulated PBMC cultured with antibodies A2_#l and A2_#2.
• Figure 16 depicts the proliferation of CD4 T cells cultured with antibodies A2_#l and A2_#2.
• Figure 17 depicts INFy secretion in Mixed Lymphocyte reaction cultured with antibodies A2_#l and A2_#2.
• the interaction of PD-1 on immune cells with PD-L1 inhibits proliferation and cytokine production by immune cells.
• PD-L1 is also inducible and upregulated in various tissues, including cancer. Together, PD-1 and PD-L1 play a role in immunosuppression.
• the invention provides novel antibodies or antigen binding fragments of such antibodies that bind to PD-1 and block the interaction with PD-L1. In embodiments of the invention, the antibodies reduce or inhibit immunosuppression.
• Novel antibodies of the invention are set forth in Table 1 and the
• sequence listing which set forth amino acid sequences of heavy and light chain CDRs (identified according to the identification systems of Kabat and Chothia), as well as complete heavy and light chain variable region.
• the first two heavy chain CDRs are identified according to the common systems of Kabat and Chothia, which provide distinct, but overlapping locations for the CDRs.
• a comparison of the numerous heavy and light chains shows a significant similarity among many of the CDR sequences. Accordingly, it would be expected that many of the CDRs can be mixed and matched among the sequences.
• the antibodies can have one or more amino acid substitutions, deletions, insertions, and/or additions.
• the antibodies comprise one of the above-mentioned heavy chain variable domains and one of the above-mentioned light chain variable domains.
• the PD-1 antibodies or binding fragments thereof comprise one or more CDRs or one or more variable domains with an amino acid sequence at least 85% at least 90%, at least 95%, at least 97%, at least 98%, or at least 99%, identical to the CDR and variable domain sequences set forth in Table 1.
• Identity refers to the number or percentage of identical positions shared by two amino acid or nucleic acid sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
• substantially identical means an amino acid sequence which differs only by conservative amino acid substitutions, for example, substitution of one amino acid for another of the same class (e.g., valine for glycine, arginine for lysine, etc.) or by one or more non-conservative substitutions, deletions, or insertions located at positions of the amino acid sequence which do not destroy the function of the protein.
• Amino acid substitutions can be made, in some cases, by selecting substitutions that do not differ significantly in their effect on maintaining (a) the structure of the peptide backbone in the area of the substitution, (b) the charge or hydrophobicity of the molecule at the target sit; or (c) the bulk of the side chain.
• residues can be divided into groups based on side-chain properties; (1) hydrophobic amino acids (norleucine, methionine, alanine, valine, leucine, and isoleucine); (2) neutral hydrophilic amino acids (cysteine, serine, and threonine); (3) acidic amino acids (aspartic acid and glutamic acid); (4) basic amino acids (asparagine, glutamine, histidine, lysine, and arginine); (5) amino acids that influence chain orientation (glycine and proline); and (6) aromatic amino acids (tryptophan, tyrosine, and phenylalanine). Substitutions made within these groups can be considered conservative substitutions.
• substitutions include, without limitation, substitution of valine for alanine, lysine for arginine, glutamine for asparagine, glutamic acid for aspartic acid, serine for cysteine, asparagine for glutamine, aspartic acid for glutamic acid, proline for glycine, arginine for histidine, leucine for isoleucine, isoleucine for leucine, arginine for lysine, leucine for methionine, leucine for phenyalanine, glycine for proline, threonine for serine, serine for threonine, tyrosine for tryptophan, phenylalanine for tyrosine, and/or leucine for valine.
• the amino acid sequence is at least 80%, or at least 85%, or at least 90%), or at least 95% identical to an amino acid sequence disclosed herein.
• Methods and computer programs for determining sequence similarity are publically available, including, but not limited to, the GCG program package (Devereux et al., Nucleic Acids Research 12: 387, 1984), BLASTP, BLASTN, FASTA (Altschul et al., J. Mol. Biol. 215:403 (1990), and the ALIGN program (version 2.0).
• the well-known Smith Waterman algorithm may also be used to determine similarity.
• BLAST program is publicly available from NCBI and other sources (BLAST Manual, Altschul, et al., NCBI LM NIH, Bethesda, Md. 20894; BLAST 2.0 at http://www.ncbi.nlm.nih.gov/blast/). In comparing sequences, these methods account for various substitutions, deletions, and other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.
• Antibodies of the invention also include those for which binding
• CDRs are mutated in a variety of ways. One way is to randomize individual residues or combinations of residues so that in a population of otherwise identical antigen binding sites, all twenty amino acids are found at particular positions. Alternatively, mutations are induced over a range of CDR residues by error prone PCR methods (see, e.g., Hawkins et al., J. Mol. Biol, 226: 889-896 (1992)).
• phage display vectors containing heavy and light chain variable region genes may be propagated in mutator strains of E. coli (see, e.g., Low et al., J. Mol. Biol, 250: 359-368 (1996)). These methods of mutagenesis are illustrative of the many methods known to one of skill in the art.
• antibodies which comprise human constant domain sequences are preferred.
• the antibodies may be or may combine members of any immunoglobulin class, such as IgG, IgM, IgA, IgD, or IgE, and the subclasses thereof.
• the antibody class may be selected to optimize effector functions ⁇ e.g., complement dependent cytotoxicity (CDC) and antibody dependent cellular cytotoxicity (ADCC)) of natural antibodies.
• Certain embodiments of the invention involve the use of PD-1 -binding antibody fragments.
• An Fv is the smallest fragment that contains a complete heavy and light chain variable domain, including all six hypervariable loops (CDRs). Lacking constant domains, the variable domains are noncovalently associated.
• the heavy and light chains may be connected into a single polypeptide chain (a "single-chain Fv" or "scFv") using a linker that allows the V H and V L domains to associate to form an antigen binding site.
• the linker is (Gly-Gly-Gly-Gly-Ser) 3 . Since scFv fragments lack the constant domains of whole antibodies, they are considerably smaller than whole antibodies. scFv fragments are also free of normal heavy-chain constant domain interactions with other biological molecules which may be undesired in certain embodiments.
• Fragments of an antibody containing V H , V L , and optionally C L , C H 1, or other constant domains can also be used.
• Monovalent fragments of antibodies generated by papain digestion are referred to as Fab and lack the heavy chain hinge region.
• Fragments generated by pepsin digestion, referred to as F(ab') 2 retain the heavy chain hinge and are divalent. Such fragments may also be recombinantly produced.
• Many other useful antigen-binding antibody fragments are known in the art, and include, without limitation, diabodies, triabodies, single domain antibodies, and other monovalent and multivalent forms.
• the invention further provides multivalent antigen-binding proteins, which can be in the form, without limitation, of antibodies, antigen-binding fragments thereof, and proteins comprising all or part of antigen-binding portions of antibodies.
• Multivalent antigen-binding proteins may be monospecific, bispecific, or multispecific.
• the term specificity refers to the number of different types of antigenic determinants to which a particular molecule can bind. If an immunoglobulin molecule binds to only one type of antigenic determinant, the immunoglobulin molecule is monospecific. If the immunoglobulin molecule binds to different types of antigenic determinants then the immunoglobulin molecule is multispecific.
• the PD-1 binding protein has an on rate constant (Kon) of at least about lC ⁇ M ' V 1 ; at least about 10 3 M "1 s "1 ; at least about lo f 1 ; at least about 10 5 M “1 s "1 ; or at least about lO'TVI ' V 1 , as measured by surface plasmon resonance.
• the PD-L1 binding protein has an on rate constant (Kon) between
• the PD-1 binding protein has an off rate constant (Koff) of at most about 10 ' V 1 ; at most about 10 ' V 1 ; at most about lO ' V 1 ; or at most about 10 ' V 1 , as measured by surface plasmon resonance.
• the PD-L1 binding protein has an off rate constant (Koff) of 10 ' Y 1 to 10 ' Y 1 ; of 10 ' Y 1 to 10 ' V 1 ; or of 10 ' Y 1 to 10 ' Y 1 , as measured by surface plasmon resonance.
• the PD-1 binding protein has a dissociation constant (K D ) of at most about 10 "7 M; at most about 10 "8 M; at most about 10 "9 M; at most about 10 "10 M; at most about 10 "U M; at most about 10 "12 M; or at most 10 "13 M.
• the binding protein has a dissociation constant (K D ) to its targets of 10 " M to 10 " M; of 10 " M to 10 "9 M; of 10 "9 M to 10 "10 M; of 10 "10 M to 10 "U M; of 10 "U M to 10 "12 M; or of 10 "12 M to 10 "13 M.
• the binding protein described herein may be a conjugate further comprising an imaging agent, a therapeutic agent, or a cytotoxic agent.
• the imaging agent is a radiolabel, an enzyme, a fluorescent label, a luminescent label, a bioluminescent label, a magnetic label, or biotin.
• the radiolabel is: 3 H, 14 C, 35 S, 90 Y, 99 Tc, m In, 125 I, 131 I, 177 Lu, or 153 Sm.
• the therapeutic or cytotoxic agent is an anti-metabolite, an alkylating agent, an antibiotic, a growth factor, a cytokine, an anti-angiogenic agent, an anti-mitotic agent, an anthracycline, toxin, or an apoptotic agent.
• an anti-metabolite an alkylating agent
• an antibiotic an antibiotic
• a growth factor a cytokine
• an anti-angiogenic agent an anti-mitotic agent
• an anthracycline an anthracycline
• toxin an apoptotic agent.
• immunostimulatory cytokines are of particular importance.
• the PD-l-binding portion of the molecule is an antigen- binding domain of an antibody.
• an antibody Several novel antibody heavy and light chain variable domains and antibodies that include them are provided.
• the PD- l-binding portion can be any agent that binds to PD-1 and blocks immunosuppression. These include anti-PD-1 antibodies and fragments, not limited to those novel antibodies disclosed herein, as well as peptides and proteins derived from PD-L1, the natural ligand of PD-1.
• the anti-PD-1 antibodies of the invention where used in a mammal for the purpose of prophylaxis or treatment, will be administered in the form of a composition additionally comprising a pharmaceutically acceptable carrier.
• suitable pharmaceutically acceptable carriers include, for example, one or more of water, saline, phosphate buffered saline, dextrose, glycerol, sucrose, polysorbate, ethanol and the like, as well as combinations thereof.
• Pharmaceutically acceptable carriers may further comprise minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the antibodies.
• a therapeutically effective amount of an antibody or antibody fragment, of the invention is administered to a mammal in need thereof.
• administering means delivering the antibodies of the present invention to a mammal by any method that may achieve the result sought. They may be administered, for example, intravenously or intramuscularly. Although the exemplified antibodies of the invention are particularly useful for administration to humans, they may be administered to other mammals as well.
• mammal as used herein is intended to include, but is not limited to, humans, laboratory animals, domestic pets and farm animals.
• “Therapeutically effective amount” means an amount of antibody of the present invention that, when administered to a mammal, is effective in producing the desired therapeutic effect, such as inhibiting kinase activity.
• Antibodies of the invention are useful for inhibiting tumors and other neoplastic diseases, as well as treating other pathologic conditions associated with
• Tumors that can be treated include primary tumors, metastatic tumors, and refractory tumors.
• Refractory tumors include tumors that fail to respond or are resistant to treatment with chemotherapeutic agents alone, antibodies alone, radiation alone or combinations thereof.
• Refractory tumors also encompass tumors that appear to be inhibited by treatment with such agents, but recur up to five years, sometimes up to ten years or longer after treatment is discontinued.
• the antibodies are effective for treating vascularized tumors and tumor that are not vascularized, or not yet substantially vascularized.
• Examples of solid tumors which may be accordingly treated include breast carcinoma, lung carcinoma, colorectal carcinoma, pancreatic carcinoma, glioma and lymphoma.
• Some examples of such tumors include epidermoid tumors, squamous tumors, such as head and neck tumors, colorectal tumors, prostate tumors, breast tumors, lung tumors, including small cell and non-small cell lung tumors, pancreatic tumors, thyroid tumors, ovarian tumors, and liver tumors.
• Other examples include Kaposi's sarcoma, CNS
• neoplasms neuroblastomas, capillary hemangioblastomas, meningiomas and cerebral metastases, melanoma, gastrointestinal and renal carcinomas and sarcomas,
• vascularized skin cancers for which the antagonists of this invention are effective include squamous cell carcinoma, basal cell carcinoma and skin cancers that can be treated by suppressing the growth of malignant keratinocytes, such as human malignant keratinocytes.
• non-solid tumors include leukemia, multiple myeloma and lymphoma.
• the tumor may be unresponsive to cytokines, such as IL15.
• leukemias include acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), erythrocytic leukemia or monocytic leukemia.
• lymphomas include Hodgkin's and non-Hodgkin's lymphoma.
• the PD-1 antibodies of the invention are also used in the treatment of viral infections.
• PD-1 expression on T cells correlates with viral load in HIV and HCV infected patients and PD-1 expression has been identified as a marker for exhausted virus-specific CD8+ T cells.
• PD-1 + CD8 + T cells show impaired effector functions and PD-1 associated T cell exhaustion which can be restored by blocking the PD-1/PD-L1 interaction. This results in recovery of virus-specific CD8+ T cell mediated immunity, indicating that interrupting PD-1 signaling using an antagonistic antibody restores T-cell effector functions.
• Immunotherapy based on the blockade of PD-1/PD-L1 results in breakdown of T-cell tolerance not only to tumor antigens, but also provides a strategy to reactivate virus-specific effector T cells and eradicate pathogens in chronic viral infections. Accordingly, the antibodies of the invention are useful to treat chronic viral infections, including, without limitation, HCV and HIV, and lymphocytic choriomeningitis virus (LCMV).
• LCMV lymphocytic choriomening
• the antibodies of the invention can be advantageously administered with second agents to patients in need thereof.
• an antibody of the invention is administered to a subject with an anti-neoplastic agent.
• an antibody of the invention is administered to a subject with an angiogenesis inhibitor. In some embodiments, an antibody of the invention is administered with an antiinflammatory agent or an immunosuppressant.
• Antineoplastic agents include cytotoxic chemotherapeutic agents, targeted small molecules and biological molecules, and radiation.
• chemotherapeutic agents include cisplatin, dacarbazine (DTIC), dactinomycin, irinotecan, mechlorethamine (nitrogen mustard), streptozocin, cyclophosphamide, carmustine (BCNU), lomustine (CCNU), doxorubicin (adriamycin), daunorubicin, procarbazine, mitomycin, cytarabine, etoposide, methotrexate, 5-fluorouracil, vinblastine, vincristine, bleomycin, paclitaxel (taxol), docetaxel (taxotere), aldesleukin, asparaginase, busulfan, carboplatin, cladribine, dacarbazine, floxuridine, fludarabine, hydroxyurea, ifo
• Targeted small molecules and biological molecules include, without limitation, inhibitors of components of signal transduction pathways, such as modulators of tyrosine kinases and inhibitors of receptor tyrosine kinases, and agents that bind to tumor- specific antigens.
• growth factor receptors involved in tumorigenesis are the receptors for platelet-derived growth factor (PDGFR), insulin-like growth factor (IGFR), nerve growth factor (NGFR), and fibroblast growth factor (FGFR), and receptors of the epidermal growth factor receptor family, including epidermal growth factor receptor (EGFR, also known as erbBl), HER2 (erbB2), erbB3, and erbB4.
• EGFR antagonists include antibodies that bind to EGFR or to an EGFR ligand, and inhibit ligand binding and/or receptor activation.
• the agent can block formation of receptor dimers or heterodimer with other EGFR family members.
• Ligands for EGFR include, for example, EGF, TGF-a amphiregulin, heparin-binding EGF (HB-EGF) and betaregullulin.
• An EGFR antagonist can bind externally to the extracellular portion of EGFR, which may or may not inhibit binding of the ligand, or internally to the tyrosine kinase domain.
• EGFR antagonists further include agents that inhibit EGFR-dependent signal transduction, for example, by inhibiting the function of a component of the EGFR signal transduction pathway.
• agents that inhibit EGFR-dependent signal transduction for example, by inhibiting the function of a component of the EGFR signal transduction pathway.
• EGFR antagonists that bind EGFR include, without limitation, biological molecules, such as antibodies (and functional equivalents thereof) specific for EGFR, and small molecules, such as synthetic kinase inhibitors that act directly on the cytoplasmic domain of EGFR.
• Small molecule and biological inhibitors include inhibitors of EGFR, including gefitinib, erlotinib, and cetuximab, inhibitors of FIER2 (e.g., trastuzumab, trastuzumab emtansine (trastuzumab-DMl; T-DMl) and pertuzumab), anti-VEGF antibodies and fragments (e.g., bevacizumab), antibodies that inhibit CD20 (e.g., rituximab,
• ibritumomab anti-VEGFR antibodies (e.g., ramucirumab (FMC-1121B), FMC-1C11, and CDP791), anti -PDGFR antibodies, and imatinib.
• Small molecule kinase inhibitors can be specific for a particular tyrosine kinase or be inhibitors of two or more kinases.
• the compound N-(3,4-dichloro-2-fluorophenyl)-7-( ⁇ [(3aR,6aS)-2- methyloctahydrocyclopenta[c]pyrrol-5-yl]methyl ⁇ oxy)-6-(methyloxy)quinazolin-4-amine (also known as XL647, EXEL-7647 and KD-019) is an in vitro inhibitor of several receptor tyrosine kinases (RTKs), including EGFR, EphB4, KDR (VEGFR), Flt4 (VEGFR3) and ErbB2, and is also an inhibitor of the SRC kinase, which is involved in pathways that result in nonresponsiveness of tumors to certain TKIs.
• RTKs receptor tyrosine kinases
• EGFR epigallocate
• EphB4 EphB4
• Flt4 Flt4
• ErbB2 ErbB2
• treatment of a subject in need comprises administration of a rh
• Dasatinib (BMS-354825; Bristol-Myers Squibb, New York) is another orally bioavailable, ATP-site competitive Src inhibitor. Dasatanib also targets Bcr-Abl (FDA- approved for use in patients with chronic myelogenous leukemia (CML) or Philadelphia chromosome positive (Ph+) acute lymphoblastic leukemia (ALL)) as well as c-Kit, PDGFR, c-FMS, EphA2, and SFKs.
• Bcr-Abl FDA- approved for use in patients with chronic myelogenous leukemia (CML) or Philadelphia chromosome positive (Ph+) acute lymphoblastic leukemia (ALL)
• CML chronic myelogenous leukemia
• ALL Philadelphia chromosome positive
• c-Kit c-Kit
• PDGFR chronic myelogenous leukemia
• c-FMS Philadelphia chromosome positive
• EphA2 EphA
• a PD-1 antibody of the invention is used in combination with an anti-viral agent to treat a chronic virus infection.
• an anti-viral agent for example, to treat HCV, the following agents can be used.
• HCV protease inhibitors include, without limitation, boceprevir, telaprevir (VX-950), ITMN-191, SCH-900518, TMC-435, BI-201335, MK-7009, VX-500, VX-813, BMS790052, BMS650032, and VBY376.
• HCV nonstructural protein 4B (NS4B) inhibitors include, but are not limited to, clemizole, and other NS4B-RNA binding inhibitors, including but not limited to benzimidazole RBIs (B-RBIs) and indazole RBIs (I- RBIs).
• HCV nonstructural protein 5A (NS5A) inhibitors include, but are not limited to, BMS-790052, A-689, A-831, EDP239, GS5885, and PP1461.
• HCV polymerase (NS5B) inhibitors include, but are not limited to nucleoside analogs (e.g., valopicitabine, R1479, R1626, R7128), nucleotide analogs (e.g., IDX184, PSI-7851, PSI-7977, and non-nucleoside analogs (e.g., filibuvir, HCV-796, VCH-759, VCH-916, ANA598, VCH-222 (VX-222), BI- 207127, MK-3281, ABT-072, ABT-333, GS9190, BMS791325).
• nucleoside analogs e.g., valopicitabine, R1479, R1626, R7128
• nucleotide analogs e.g., IDX184, PSI-7851, PSI-7977
• non-nucleoside analogs e.g., filibuvir, HCV-796, VCH-759,
• ribavirin or a ribavirin analog such as Taribavirin (viramidine; ICN 3142), Mizoribine, Merimepodib (VX- 497), Mycophenolate mofetil, and Mycophenolate can be used.
• a dose of an antibody of the invention is administered to a subject every day, every other day, every couple of days, every third day, once a week, twice a week, three times a week, or once every two weeks.
• two, three or four doses of a compound or a composition is administered to a subject every day, every couple of days, every third day, once a week or once every two weeks.
• a dose(s) of a compound or a composition is administered for 2 days, 3 days, 5 days, 7 days, 14 days, or 21 days.
• a dose of a compound or a composition is administered for 1 month, 1.5 months, 2 months, 2.5 months, 3 months, 4 months, 5 months, 6 months or more.
• Methods of administration include but are not limited to parenteral, intradermal, intravitrial, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, oral, sublingual, intranasal, intracerebral, intravaginal, transdermal, transmucosal, rectally, by inhalation, or topically, particularly to the ears, nose, eyes, or skin.
• the mode of administration is left to the discretion of the practitioner. In most instances, administration will result in the release of a compound into the bloodstream.
• intravitrial administration of biological agents is preferred.
• a compound may be desirable to administer a compound locally. This may be achieved, for example, and not by way of limitation, by local infusion, topical application, by injection, by means of a catheter, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. In such instances, administration may selectively target a local tissue without substantial release of a compound into the bloodstream.
• Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent, or via perfusion in a fluorocarbon or synthetic pulmonary surfactant.
• a compound is formulated as a suppository, with traditional binders and vehicles such as triglycerides.
• a compound is delivered in a vesicle, in particular a liposome (See Langer, 1990, Science 249: 1527 - 1533; Treat et al., in Liposomes in the Therapy of Infectious Disease and Bacterial infection, Lopez -Berestein and Fidler (eds.), Liss, New York, pp. 353 - 365 (1989); Lopez Berestein, ibid., pp. 317 - 327; see generally ibid.).
• a liposome See Langer, 1990, Science 249: 1527 - 1533; Treat et al., in Liposomes in the Therapy of Infectious Disease and Bacterial infection, Lopez -Berestein and Fidler (eds.), Liss, New York, pp. 353 - 365 (1989); Lopez Berestein, ibid., pp. 317 - 327; see generally ibid.).
• a compound is delivered in a controlled release system (See, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115 - 138 (1984)). Examples of controlled-release systems are discussed in the review by Langer, 1990, Science 249: 1527 - 1533 may be used.
• a pump may be used (See Langer, supra; Sefton, 1987, CRC Crit. Ref. Biomed. Eng. 14:201; Buchwald et al., 1980, Surgery 88:507; Saudek et al., 1989, N. Engl. J. Med. 321 :574).
• a pump may be used (See Langer, supra; Sefton, 1987, CRC Crit. Ref. Biomed. Eng. 14:201; Buchwald et al., 1980, Surgery 88:507; Saudek et al., 1989, N. Engl. J. Med. 321 :574).
• polymeric materials can be used (See Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Florida (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, 1983, J. Macromol. Sci. Rev. Macromol. Chem. 23 :61; See also Levy et al., 1985, Science 228: 190; During et al., 1989, Ann. Neurol. 25:351; Howard et al., 1989, J. Neurosurg. 71 : 105).
• Anti-PD-1 antibodies with high affinity were obtained using a phage display library.
• phage Fabs amplified from Dyax libraries were panned on soluble PD-l-Fc captured by biotin-anti-hFc Ab and magnetic strep-beads.
• phage Fabs amplified from the Dyax libraries were panned on tube immobilized PD-l-Fc for the first round, and then panned on PD-1 transfected 293 cells for second round.
• phage Fabs amplified from the Dyax libraries were panned on soluble biotin-PD-l-Fc and captured by magnetic strep-beads.
• R3A1, R3A2, R4B3, R3B7, and R3D6 Five unique clones (R3A1, R3A2, R4B3, R3B7, and R3D6) were converted to IgG for the further characterization.
• the amino acid sequences of four of these variants (R3A1, R3A2, R4B3, and R3D6) are set forth in the sequence listing as indicated in rows 1-4 of Table 1.
• the binding activity of the five antibodies was examined using dose-response ELISA.
• the serially diluted antibodies were added to immobilized hPD-l-Fc and detected by HRP conjugated anti-hlgG Fab specific antibody.
• the OD450 reading was plotted vs. log antibody concentration using GraphPad Prism6.
• EC50 was calculated by using "dose- response" (stimulation) variable slope (four parameters)" program.
• the antibodies were also added to immobilized mPD-l-Fc and other Fc-fusions to determine specificity for hPD-l-Fc and to immobilized anti-human IgG fc specific antibody (anti-hFc Ab) to check the accuracy of the concentration measurement.
• All five antibodies can bind to soluble human PD-l-Fc (Fig. 5) and block ligand PD-L1 binding to PD-1 (Fig. 6).
• R4B3 can also bind to murine PD-1 (Fig. 7), and R3B7 has low binding affinity to other Fc-fusions (Figs. 2-4).
• R3A1, R3A2, R4B3, and R3D6 were carried forward for affinity maturation through light chain shuffling.
• Light chain shuffling was used to increase the affinity of the four lead antibodies. More particularly, the heavy chains of R3A1, R3A2, R4B3, and R3D6 were paired with ⁇ light chain pool to build light chain shuffling libraries. The libraries were panned for higher affinity antibodies. The ELISA positive clones were sequenced. The unique clones were compared by competition ELISA. The amino acid sequences of these variants are set forth the sequence listing as indicated in rows 5-56 of Table 1.
• CM5 chip was equilibrated in running buffer HBSEP (running buffer) at ⁇ /ml.
• HBSEP running buffer
• Two flow cells of a CM5 chip were activated with 1 : 1 NHS/EDC injection for five minutes.
• the second flow cell was immobilized with 5 ⁇ g/ml of hPD-Llfc diluted in 10 mM sodium acetate buffer pH 5 to reach 30-50RU of immobilized protein.
• the surfaces were subsequently blocked with a 5 minute injection of ethanolamine followed by a 5 minute injection of NSB reducer.
• the binding activity of the lead candidate antibodies to surface expressed PD- 1 or PD-L1 in HEK293 transfectant cells and CD4 and CD8 T cells was evaluated by flow cytometry using Guava EasyCyteTM HT Sampling Flow Cytometer (EMD Millipore) per manufacture instruction. Purified human CD4 and CD8 T cells were activated by anti-CD3 antibody coated beads at 1 :5 ratio of bead to T cells for 4 days prior to staining with anti-PD- 1 antibodies. R-phycoerythrin-conjugated goat anti -human IgG (Cat# 109-116-098, Jackson ImmunoResearch) was used as secondary antibody to detect the binding of primary antibodies.
• Results for HEK293 cells are shown in Fig. 11, for CD4 T cells in Fig. 12, and CD8 T cells in Fig. 13.
• Anti-PD-1 antibodies A2_#l and A2_#2 were verified to have comparable activity to increase Thl cytokine secretion.
• PBMCs were isolated from LeukoPak (an enriched leukapheresis containing highly concentrated blood cells including monocytes, lymphocytes, platelets, plasma, as well as red cells using Histopaque-1077 (Sigma) per manufacture instruction.
• PBMCs were cultured at 2 x 10 4 per well in 96 well plate containing FMDM (Iscove's Modified Dulbecco's Medium, supplemented 2 mM Glutamine, 25 mM HEPES, 3.024 g/L Sodium Bicarbonate, Technologies cat# 31980-097) and 10% Fetal Bovine Serum (FBS, cat# SH30396.03, HyClone) and activated by 0.1 ug/mL SEB
• FMDM Scove's Modified Dulbecco's Medium, supplemented 2 mM Glutamine, 25 mM HEPES, 3.024 g/L Sodium Bicarbonate, Technologies cat# 31980-097
• Fetal Bovine Serum FBS, cat# SH30396.03, HyClone
• Results for IL-2 secretion are shown in Fig. 14, and results for IFNy are shown in Fig. 15. Signficant increases in the levels of IFNy were observed in cultures with the lead candidate anti-PD-1 antibodies A2_#l and A2_#2.
• Anti-PD-1 antibodies A2_#l and A2_#2 were verified to have comparable activity to increase the proliferation of CD4 T cells.
• Human CD4 T cells isolated from whole blood were stimulated with anti-CD3 antibody and PD-Ll-Fc coated beads in the presence of anti-PD-1 antibodies for 4 days. Proliferation was measured by proliferative marker Ki67 staining.
• Results are shown in Fig. 16. Significant increases in the proliferation of CD4 T cells were observed in cultures with anti-PD-1 antibodies A2_#l and A2_#2.
• Anti-PD-1 antibodies A2_#l and A2_#2 were verified to have comparable activity to increase Thl cytokine secretion in Mixed Lymphocyte reactions.
• Immature monocyte-derived dendritic cells (mo-DC) were generated by culturing CD 14 positive cells in EVIDM supplemented with 10% FBS with 150 ng/ml GM-CSF and 50 ng/mL IL-4 for 6 to 7 days.
• CD4 positive cells were negatively isolated from whole blood using RosetteSep human CD4 enrichment kit (StemCell Technologies).
• Mo-DC and CD4 positive cells were then co-cultured at a ratio 1 : 10 of mo-DC to CD4 cells, respectively.
• To assess blocking function of anti-PD-1 antibodies increasing amount of anti-PD-1 antibodies was added in the beginning of co-culture. At day 7, the supernatants were collected for measurements of secreted IFNy by ELISA.
• Results are shown in Fig. 17. Significant increases in the levels of IFNy were observed in cultures with the variants of anti-PD-1 antibodies A2 #1 and A2 #2.

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